Science review - 2009 week 48/49

RNA
Sequence based multiple aligment of RNA
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/24/3236?rss=1

RNA structure's role in pre mRNA splicing
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCV-4XV2JFP-1&_user=1676895&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000054205&_version=1&_urlVersion=0&_userid=1676895&md5=ae559eb8ed285ebd773e3cccf143c617

Nobel prize for the ribosome - an Essay
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCV-4XV8H85-1&_user=1676895&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000054205&_version=1&_urlVersion=0&_userid=1676895&md5=1f19b7fbd999951ebaaca7301a8c198b

New big RNAs identified in the ocean
http://www.nature.com/nature/journal/v462/n7273/full/7273543a.html


Molecular Biology
The minimal cell - an essay (more or less) by Venter et al.
http://www.nature.com/msb/journal/v5/n1/full/msb200989.html

Prions - responible for even more neurodegenerative diseases?
http://www.sciencemag.org/cgi/content/full/326/5958/1337?rss=1


Drug discovery
Pharmaceutical output - as constant as ever
http://www.nature.com/nrd/journal/v8/n12/full/nrd2961.html


Teaching
Connecting wired science to the real world seems to result in better students
http://www.sciencemag.org/cgi/content/full/326/5958/1410?rss=1

Hadoop and Life Sciences - some cool talks from the Hadoop Conference in NY

General talk about life sciences at EC2 using Hadoop
http://vimeo.com/7351342

Protein Alignment in the Cloud
http://vimeo.com/7115816

Nice :)

Science review - 2009 week 45, 46 and 47

Gossip
Nature vs. MAD:
http://www.nature.com/nature/journal/v462/n7270/full/462242a.html
Alberts about a better funding and better science
http://www.sciencemag.org/cgi/content/full/326/5957/1163?rss=1
Alberts about PhD students lost in translation- with advice and hints - very cool:
http://www.sciencemag.org/cgi/content/full/326/5955/916?rss=1
A true letter about (IMHO) a huge problem in Science: Management
http://www.sciencemag.org/cgi/content/full/326/5956/1062-a?rss=1
A super cool essay about academia, industry and skills:
http://www.nature.com/nrm/journal/v10/n12/full/nrm2796.html


Next generation sequencing:
Bing - not from Microsoft  - a framework to manage and evaluate data from NGS:
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WHD-4XPYXJY-1&_user=1676895&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000054205&_version=1&_urlVersion=0&_userid=1676895&md5=1b9b25e7610687136d0ba1e4fc3119bb


Binding promiscuity
An introduction by Nature:
http://www.nature.com/nature/journal/v462/n7270/full/462167a.html
and a cool paper:
http://www.nature.com/nature/journal/v462/n7270/full/462167a.html
and a paper I think is worth mentioning in this case:

Cloud computing in life sciences
Aligning and SNP calling in the cloud
http://genomebiology.com/2009/10/11/R134

Transcription factors and regulation
State of the Art:
http://www.nature.com/msb/journal/v5/n1/full/msb200988.html

RNA structure
TPP riboswitch - ligand free
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4XPYXRM-3&_user=1676895&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000054205&_version=1&_urlVersion=0&_userid=1676895&md5=646fe1d1ba339fa66c8116362ca853dc

Virus RNA packaging mediated by an RNA switch:
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4XPYXRM-5&_user=1676895&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000054205&_version=1&_urlVersion=0&_userid=1676895&md5=1ec65e5a1a729a33ac8fc39a3f89400f

Ago silencing complex - from the Patel / Tuschl labs:
http://www.nature.com/nature/journal/v461/n7265/full/nature08434.html

Politics
About the Antarctic Treaty - I hope it lasts as ice is melting and states can expand their greed for natural resources easily
http://www.nature.com/nature/journal/v462/n7272/full/462412a.htm


Protein protein docking 
Knapp about selecting the most likely native docking decoy
http://www3.interscience.wiley.com/cgi-bin/fulltext/122617886/HTMLSTART


The future of publication

Article-Level Metrics and the Evolution of Scientific Impact - PLoS Biology:http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000242?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+plosbiology%2FNewArticles+%28PLoS+Biology%3A+New+Articles%29&utm_content=Google+Reader
Public access is cool:
http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000237?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+plosbiology%2FNewArticles+%28PLoS+Biology%3A+New+Articles%29&utm_content=Google+Reader

Drug discovery - book recommendations collected by Derek Lowe

really cool:
http://pipeline.corante.com/archives/2009/11/28/recommended_books_for_medicinal_chemists_part_one.php
thanks Derek and contributors!

It wasn't me!

Must have been somebody else. For instance: The genes in me :)

http://www.nature.com/news/2009/091030/full/news.2009.1050.html

My bet: Berlusconi has some genes for bribing people what means he is not really responsible for his wrongdoings. So this is clearly a preparation for his upcoming trials.

Btw - the Italians have a gene that forces them to vote for incapable presidents. And the germans... well... ok...

Science review - 2009 week 44

Gossip:
Hwang moves on:
http://www.sciencemag.org/cgi/content/full/326/5953/650-a?rss=1

Nanotechnology and Russia:
http://www.nature.com/nature/journal/v461/n7267/full/4611028a.html

Hunting is fun:
http://www.sciencemag.org/cgi/content/full/326/5952/506?rss=1

After the HIV vaccine revolution Nature did not like the hype:
http://www.nature.com/nature/journal/v461/n7268/full/4611174a.html


Sequencing:
A cool review about cance genome sequencing:
http://hmg.oxfordjournals.org/cgi/content/full/18/R2/R163

Sequencing and sorting - that's cool:
http://www.nature.com/nmeth/journal/v6/n10/abs/nmeth.1370.html


Structural Biology:
Fast strctural comparisons based on vectors:
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/21/2843?rss=1

and also:
Algorithms for the optimal superposition of proteins...:
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/21/2751?rss=1

A good starting point provided by the PLoS ONE for the SGC:
http://www.plosone.org/article/browseIssue.action?issue=info%3Adoi%2F10.1371%2Fissue.pone.c01.i04


Systems Biology:
Kitano on networks and implications for drug design:
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000550

Science review - 2009 week 43

Glamour:
Nature about scientists talking journalists fooling them and how to react (and how not):
http://www.nature.com/nature/journal/v461/n7266/full/461848a.html


About the Polymath project, where a mathematic problem was solved using an open approach with wikis and so on - really cool:
http://www.nature.com/nature/journal/v461/n7266/full/461879a.html

and then you could also read an article about Google Wave and it's impact for science (accoring to the author - I am less sure there will be an impact).:
http://www.nature.com/nature/journal/v461/n7266/full/461881a.html

KAUST - the universtiy in the desert (and in a dictatorship like kingdom):
http://www.sciencemag.org/cgi/content/full/326/5951/354?rss=1

PLoS Medicine - refocuses and adopts new interesting concepts - from Twitter to PLoS Currents:
http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.1000167


Methylation:
An interview with one of founders of "methylation": Adrian Bird
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000667

Nice debate about how methylation patterns are generated:
http://www.nature.com/nrg/journal/v10/n11/full/nrg2651.html

RNA:
Three way junctions in RNA - found in many RNA structures:
http://rnajournal.cshlp.org/content/15/11/1949.short?rss=1


Biology and Chemistry:
Nature Chemical Biology about the downsides of an reductionist apporach - Cells are more than the simple sum of it's part (systems biology?)
http://www.nature.com/nchembio/journal/v5/n11/full/nchembio.258.html
http://www.nature.com/nchembio/journal/v5/n11/full/nchembio.241.html

RNA and Chromatin structure control a range of biological processes - an overview:
http://www.nature.com/nrg/journal/v10/n11/full/nrg2692.html

Structual Biology:
Oberving biology in atomic resolution in real time - cool:
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCV-4XGTJ7J-1&_user=1676895&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000054205&_version=1&_urlVersion=0&_userid=1676895&md5=635a71eaba1f693b8a8e71044c882860

Bioinformatics:
A new twist for determining possible drug targets based on kinetic network models:
http://www.biomedcentral.com/1471-2105/10/344

Know the CPU architecture and make BLAST faster:
http://www.biomedcentral.com/1471-2105/10/329

Riboswitch detection on sequence level:
http://www.biomedcentral.com/1471-2105/10/325

Glad to know that the PSI is advancing

PSI (Protein Structure initiative) is an initiative that aims to shed light on proteins with roughly unknown function.

There is a new videocast available from a recent meeting:
http://videocast.nih.gov/PastEvents.asp?c=4

Want to know more? Here's the FAQ:
http://www.nigms.nih.gov/Initiatives/PSI/psi_biology/psibiology_faqs.htm

And the corresponding press report is at:
http://kb.psi-structuralgenomics.org/update/2009/10/full/nw_psisgkb.2009.47.html